Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1291
Accession number AF196721
Name 93ZR72
Sampling year 1993

AF196721 isolate has foldings of [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [USE region] [227nt 3' terminus] [Complete poly(A) region] [USE, TAR, polyA] .

The region encompassing 227 nt 3' terminus

The primary sequence:

ctaaccctca gatgctgcat ataagcagct gctctttgcn tgtactgggt ctctctggtt agaccagatt tgagcctgag agctctctga ctagctgggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccat tt-agtcagtg tggaaaatct ctagca

The optimal secondary structure:

The suboptimal structures within ΔΔG ≤ 4 kcal/mole of the minimum free energy